Diamond database not made when making local database

[renVer01]

Hi,

I was trying to make a local database with the cblaster makedb command from genbank files. Everything seems to run fine, except no diamond database is made. I saw in another thread that an incorrect installation of the diamond package might be the problem, but after reinstalling I still have the same issue.

Do you have any idea what else could be the problem?

Thanks!

[Kiratrea]

I am having the same issue.

[Kiratrea]

Ok I think I solved it. I had to check my fasta file for gaps. Once I got rid of the gaps I was able to make the diamond database directly with diamond and use it with cblaster going forward.

[fjell-dev]

Having the same results also. It looks like that the fasta file output from the command contained some empty sequences and diamond could not create the database. Cblaster did not handle the error from diamond correctly and therefore there was no database created.

[renVer01]

Yes, removing empty sequences fixed the issue for me as well. Thanks!

[fjell-dev]

I used this command to remove the empty sequences in my large FASTA file sed -i 'N;/\n$/d' large_file.fasta (use at your own risk) and use the diamond makedb command successfully. The cblaster search command worked with the "manually" created diamond database, apparently.

[mvalvano]

I have encountered the same problem. cblaster makedb outputs the faster file and sqlite file but not the dmnd file. I did as fjell-dev suggested but using the command sed 'N;/\n$/d' [large_file.fasta] > [large.fasta].

[large_file.fasta] is the fasta output of cblaster [large.fasta] is the input for diamond after cleaning the empty lines, as follows: diamond makedb --in large.fasta --db myDb.dmnd

I tested cblaster search with myDb.dmnd and all worked well